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Data frame used as a data dictionary to recode common variant classification types to standardized types that can be used in oncoKB annotation.

Usage

consequence_map

Format

A data frame

variant_classification

character indicating type of mutation/variant classification as it appears in common mutation files

consequence_final_coding

final value to recode variant_classification column to

consequence_final_coding_2

final value to recode variant_classification column to

consequence_final_coding_3

final value to recode variant_classification column to

@source https://github.com/oncokb/oncokb-annotator/blob/a80ef0ce937c287778c36d45bf1cc8397539910c/AnnotatorCore.py#L118